VMD-L Mailing List

From: Darrell Kuykendall (darrellk_at_me.com)
Date: Thu Jul 24 2014 - 13:57:16 CDT

Hi, John,

I’ve attached a .zip with the requested files for ethylene.

Thanks!
Darrell


On Jul 24, 2014, at 11:19 AM, John Stone <johns_at_ks.uiuc.edu> wrote:

> Darrell,
> If you can provide a gzip/zip file that contains your GAMESS log file
> and an associated VMD saved state that loads it in the form you want to
> export to .obj, I would be happy to take a look at what may be
> going on in this case.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Jul 24, 2014 at 11:00:20AM -0400, Darrell Kuykendall wrote:
>> Hi,
>>
>> Yes. Running VMD 1.9.1 on Mavericks. I'm loading GAMESS .log files into VMD and using orbital representations, then rendering as .obj to move over to Maya.
>>
>> This afternoon, I'll be doing more testing and will post any discoveries.
>>
>> Thanks!
>> Darrell
>>
>>> On Jul 24, 2014, at 10:37 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
>>>
>>> Hi,
>>> Which version of VMD are you running presently? I'm guessing 1.9.1 based
>>> on the .mtl comment below.
>>>
>>> How are you rendering the orbitals, what file format(s) are you loading,
>>> and are you rendering a density map using an isosurface representation in
>>> VMD, or are you using the Orbital representation in concert with a GAMESS
>>> or Molden input file?
>>>
>>> Cheers,
>>> John Stone
>>> vmd_at_ks.uiuc.edu
>>>
>>>> On Wed, Jul 23, 2014 at 04:30:19PM -0400, Darrell Kuykendall wrote:
>>>> Hi, all,
>>>> I*ve been using VMD to create .obj files (among other things) for ab
>>>> initio structures, which I then bring into Maya for animation. All has
>>>> worked well until recently when I*ve begun to render orbitals as well. One
>>>> phase of an orbital always renders as a *transparent* or *ghosted*
>>>> material. I use quotes because no matter what material is assigned to this
>>>> object it remains transparent. Interestingly, if I do certain spatial
>>>> transformations in Maya, the object appears as expected (not transparent)
>>>> but as soon as it is placed back at its intended position, it goes
>>>> transparent again.
>>>> In the limited amount of troubleshooting I was able to do this afternoon,
>>>> I discovered that: 1) exporting only the properly rendered phase of a
>>>> symmetrical orbital as .obj from VMD and then copying and reflecting this
>>>> orbital in Maya works until the copy is in an exact mirror position, then
>>>> it becomes transparent and 2) there doesn*t seem to be any correlation
>>>> between the order of representation creation in VMD and which orbital gets
>>>> affected, nor the phase.
>>>> I*ll keep playing around to see what else I can discover. Incidentally, I
>>>> saw that the mtllib statement in the .obj files from VMD incorrectly
>>>> reference the associated .mtl (first letter of .mtl filename is always
>>>> missing). I can see reasons that that might be intentional though.
>>>> Thanks for any help!
>>>> D
>>>
>>> --
>>> NIH Center for Macromolecular Modeling and Bioinformatics
>>> Beckman Institute for Advanced Science and Technology
>>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>>> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
>>> http://www.ks.uiuc.edu/Research/vmd/
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>